Global identification and characterization of transcriptionally active regions in the rice genome.
Global identification and characterization of transcriptionally active regions in the rice genome.
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DOI：
10.1371/journal.pone.0000294
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发表时间：
2007-03-14
期刊：
影响因子：
3.7
通讯作者：
Deng XW
中科院分区：
文献类型：
--
作者：
Li L;Wang X;Sasidharan R;Stolc V;Deng W;He H;Korbel J;Chen X;Tongprasit W;Ronald P;Chen R;Gerstein M;Deng XW
基因组平铺微阵列研究一致记录了丰富的转录活性，超出了注释基因。然而，在基因组尺度上对假定的新转录物的系统表征和转录谱分析仍然缺乏。我们在此报告了水稻（Oryza）中鉴定出25,352和27,744个转录活性区域（TARs），这些区域未被注释外显子编码。Sativa)亚种，分别为粳稻和籼稻。非外显子TARs约占平铺阵列检测到的TARs总数的三分之二，代表了可能在粳稻和籼稻之间保守的转录本。通过在10种组织类型中使用重阵列的表达谱来验证21,018个（83%）粳稻非外显子TARs的转录，其中注释的基因和TARs分别由5个独立探针代表。随后的分析表明，约80%未分配到注释外显子上的粳稻TARs可分配到水稻基因组的各种假定功能或结构元件上，包括剪接变异体、未完全注释基因的未表征部分、反义转录本、重复基因片段和潜在的非编码rna。这些结果提供了水稻非外显子转录物的系统表征，从而扩展了水稻转录组复杂性和动态的现有观点。
Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs) not encoded by annotated exons in the rice (Oryza. sativa) subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83%) japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.
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